README_setup.sh
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README_setup.sh
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			# Create LAMMPS input files this way:
			cd moltemplate_files

			# run moltemplate

			moltemplate.sh -a "@atom:WatMW/mW 1" system.lt

			# Each atom type (eg "mW") must be assigned to an integer (because LAMMPS
			# does not understand descriptive names). Normally LAMMPS does not care what
			# these numbers are, however many-body force-fields (used in this example)
			# are an exception. Here we just want to make sure that the "mW" atom
			# type is assigned to number "1" so we use -a "@atom:WatMW/mW 1"
			# (The full-name of the atom is "WatMW/mW", not "mW", because it is part
			# of the "WatMW" molecule-object. See "watmw.lt" for details.)


			# This will generate various files with names ending in .in and *.data.
			# These files are the input files directly read by LAMMPS. Move them to
			# the parent directory (or wherever you plan to run the simulation).

			mv -f system.in* system.data ../

			# Optional:
			# The "./output_ttree/" directory is full of temporary files generated by
			# moltemplate. They can be useful for debugging, but are usually thrown away.
			rm -rf output_ttree/

			cd ../